Multi-omics and single cell characterization of cancer immunosenescence landscape.

Cellular senescence (CS) is closely related to tumor progression. However, the studies about CS genes across human cancers have not explored the relationship between cancer senescence signature and telomere length. Additionally, single-cell analyses have not revealed the evolutionary trends of malignant cells and immune cells at the CS level. We defined a CS-associated signature, called "senescence signature", and found that patients with higher senescence signature had worse prognosis. Higher senescence signature was related to older age, higher genomic instability, longer telomeres, increased lymphocytic infiltration, higher pro-tumor immune infiltrates (Treg cells and MDSCs), and could predict responses to immune checkpoint inhibitor therapy. Single-cell analysis further reveals malignant cells and immune cells share a consistent evolutionary trend at the CS level. MAPK signaling pathway and apoptotic processes may play a key role in CS, and senescence signature may effectively predict sensitivity of MEK1/2 inhibitors, ERK1/2 inhibitors and BCL-2 family inhibitors. We also developed a new CS prediction model of cancer survival and established a portal website to apply this model ( https://bio-pub.shinyapps.io/cs_nomo/ ).

Subfunctionalisation and self-repression of duplicated E1 homologues finetunes soybean flowering and adaptation.

Soybean is a photoperiod-sensitive staple crop. Its photoperiodic flowering has major consequences for latitudinal adaptation and grain yield. Here, we identify and characterise a flowering locus named Time of flower 4b (Tof4b), which encodes E1-Like b (E1Lb), a homologue of the key soybean floral repressor E1. Tof4b protein physically associates with the promoters of two FLOWERING LOCUS T (FT) genes to repress their transcription and delay flowering to impart soybean adaptation to high latitudes. Three E1 homologues undergo subfunctionalisation and show differential subcellular localisation. Moreover, they all possess self-repression capability and each suppresses the two homologous counterparts. Subfunctionalisation and the transcriptional regulation of E1 genes collectively finetune flowering time and high-latitude adaptation in soybean. We propose a model for the functional fate of the three E1 genes after the soybean whole-genome duplication events, refine the molecular mechanisms underlying high-latitude adaption, and provide a potential molecular-breeding resource.

The non-covalent and covalent interactions of whey proteins and saccharides: influencing factor and utilization in food.

During the application of Whey proteins (WPs), they often have complex interactions with saccharides (Ss), another important biopolymer in food substrate. The texture and sensory qualities of foods containing WPs and Ss are largely influenced by the interactions of WPs-Ss. Moreover, the combination of WPs and Ss is possible to produce many excellent functional properties including emulsifying properties and thermal stability. However, the interactions between WPs-Ss are complex and susceptible to some processing conditions. In addition, with different interaction ways, they can be applied in different fields. Therefore, the non-covalent interaction mechanisms between WPs-Ss are firstly summarized in detail, including electrostatic interaction, hydrogen bond, hydrophobic interaction, van der Waals force. Furthermore, the existence modes of WPs-Ss are introduced, including complex coacervates, soluble complexes, segregation, and co-solubility. The covalent interactions of WPs-Ss in food applications are often formed by Maillard reaction (dry or wet heat reaction) and occasionally through enzyme induction. Then, two common influencing factors, pH and temperature, on non-covalent/covalent bonds are introduced. Finally, the applications of WPs-Ss complexes and conjugations in improving WP stability, delivery system, and emulsification are described. This review can improve our understanding of the interactions between WPs-Ss and further promote their wider application.

A critical suppression feedback loop determines soybean photoperiod sensitivity.

Photoperiod sensitivity is crucial for soybean flowering, adaptation, and yield. In soybean, photoperiod sensitivity centers around the evening complex (EC) that regulates the transcriptional level of the core transcription factor E1, thereby regulating flowering. However, little is known about the regulation of the activity of EC. Our study identifies how E2/GIGANTEA (GI) and its homologs modulate photoperiod sensitivity through interactions with the EC. During long days, E2 interacts with the blue-light receptor flavin-binding, kelch repeat, F box 1 (FKF1), leading to the degradation of J/ELF3, an EC component. EC also suppresses E2 expression by binding to its promoter. This interplay forms a photoperiod regulatory loop, maintaining sensitivity to photoperiod. Disruption of this loop leads to losing sensitivity, affecting soybean's adaptability and yield. Understanding this loop's dynamics is vital for molecular breeding to reduce soybean's photoperiod sensitivity and develop cultivars with better adaptability and higher yields, potentially leading to the creation of photoperiod-insensitive varieties for broader agricultural applications.

A population-based study exploring association of parasomnia symptoms with sleep onset delay among school-aged children.

OBJECTIVE: Parasomnia is potentially implicated in sleep pattern and sleep architecture, however, evidence is quite limited. This study aimed to investigate the association between parasomnia symptoms and sleep onset delay among children through a large epidemiological study. METHODS: Two rounds of cross-sectional studies were conducted among 21,704 children aged 3-11; one taking place in Shanghai and the other in Sanya, Hainan province. Children's sleep characteristics were evaluated using the Children's Sleep Habits Questionnaire (CSHQ). Propensity score matching was adopted to balance the difference of covariates, and the logistic regression models were implemented to examine the associations between parasomnia symptoms and sleep onset delay. RESULTS: A total of 38.2 % of children had sleep onset delay. Parasomnias, especially non rapid eye movement (NREM) and rapid eye movement (REM) parasomnia symptoms, were associated with an increased risk of sleep onset delay (Sleep Walking: OR = 1.55; Sleep Terror: OR = 1.34; Nightmare: OR = 1.37, all p˂0.001). The similar findings were observed in stratified analyses according to sleep duration, and the association was pronounced in sleep sufficiency group (Sleep Walking: OR = 1.62; Sleep Terror: OR = 1.35; Nightmare: OR = 1.35, all p˂0.001). Moreover, a dose-dependent pattern was observed, in which cumulative parasomnia symptoms were associated with increasing risk of sleep onset delay (2 symptoms: OR = 1.19; ≥3 symptoms: OR = 1.40; by comparison with ≤1 symptom). All these findings were also similarly observed in the propensity score matching sample. Moreover, the associations were generally established in both Shanghai and Sanya children. CONCLUSIONS: Parasomnia symptoms were associated with a higher risk of sleep onset delay independently of sleep duration among children. More studies are needed to enrich the current evidence, thus further clarifying the association and interaction among different sleep parameters.

Effects of climate and environment on migratory old people with allergic diseases in China: Protocol for a Sanya cohort study.

Background: Several studies have reported that the mountain climate can alleviate asthma, however, the effect of tropical climate on migratory elderly, especially in people with respiratory or allergic diseases is unknown. Objectives: This cohort study aims to explore impact of climate and environmental changes on allergic diseases in migratory old people. Methods: In this prospective cohort study, we recruited 750 older migratory people, the majority of whom were homeowners to minimize the risk of loss to follow up. The study's inclusion criteria were elderly individuals had moved from northern China to Sanya and suffered from either asthma or allergic diseases. Prior to participation, these individuals provided informed consent and underwent baseline assessment. Subsequently, they will be followed for three years. A face-to-face interview was conducted to gather information regarding their living environment and habits. Trained investigators administered the questionnaires and performed physical examinations including height, weight, and blood pressure, while a professional respiratory doctor conducted pulmonary function tests. Blood samples were promptly tested routine blood test, liver function, kidney function, glucose, triglyceride, allergens, and inflammatory factors. Climate and environmental data were obtained from Sanya Meteorological Bureau and Ecological Environment Bureau, respectively. We primarily compared the differences of participants with asthma or allergic diseases between northern China and Sanya in southern China by Chi-square test, t-test or Wilcoxon rank-sum test. Findings: A total of 750 participants were recruited in this cohort from fourteen communities. All participants were surveyed questionnaires about health and family environment, underwent physical examinations, and collected biological samples for laboratory examinations. Novelty: This is the first study to evaluate the effects of tropical climate and environment on elderly migrants from cold regions. This study has important implication for the health tourism and aging health, especially for the elderly migrants who suffered the respiratory and allergic diseases. Furthermore, this cohort study establishes a solid foundation for investigating the influence of environmental changes on elderly migrants with allergic diseases.

Sanya climatic-treatment cohort profile: objectives, design, and baseline characteristics.

Background: The prevalence of allergic diseases has increased globally, climate and environment also have important effects on respiratory or allergic diseases. However, population-based studies investigating the impact of tropical climates and environments on migratory-bird old people (MBOP) are lacking. Methods/Design: For this prospective cohort study, we recruited 756 participants from the community in Sanya City, Hainan Province, China. In addition to the completed baseline survey, a follow-up survey will be conducted during the periods of October-December and March-April for the next 3 years of MBEPs from northern China who spend the winter in Sanya. We will continue to record the height, weight, and blood pressure of all participants, as well as lung function for those with asthma and chronic obstructive pulmonary disease (COPD). Venous blood at baseline and urine samples will be collected during follow-up. Results: A total of 756 volunteers were recruited. Their average age is 66.1 years; 32.1% of them have high-school educations, while 37.3% have graduated from college or done undergraduate studies. The top five diseases in this cohort are allergic rhinitis (57.9%); eczema, urticaria, or dermatitis (35.6%); bronchitis and bronchiectasis (35.6%); asthma (14.7%); and emphysema (11.7%). Compared with their symptoms while at their summer places of residence, rates of remission reported by participants while living in Sanya were 80.4% for allergic rhinitis, 82.3% for bronchitis and emphysema, 85.2% for asthma, 96.0% for COPD (P < 0.001). Conclusions: The baseline survey has been completed. The preliminary findings support that a tropical climate may relieve the symptoms of allergic diseases in migratory-bird old people.

Young people exposure to antibiotics: Implication for health risk and the impact from eating habits of takeaway food.

Exposure to antibiotics, mainly from animal food ingestion, may have adverse effects on human health. Takeaway food is the preferred choice for the dietary of most Chinese young people nowadays, but the relationship between takeaway eating and antibiotic exposure is not yet adequately understood. In the present study, 297 young people were recruited to collect urine samples and questionnaires with an emphasis on their takeaway eating habits. The internal exposure to 16 antibiotics and three metabolites was measured in urine samples by high-performance liquid chromatography-tandem mass spectrometry, as well as a DNA oxidative damage marker, 8-hydroxydeoxyguanosine (8-OHdG). At least one kind of antibiotic was found in over 90 % of urine samples, with total concentrations from 0.667 to 3.02 × 104 ng/mL. High exposure levels of antibiotics were more likely to be found in individuals with a larger body mass index. The concentrations of six antibiotics were significantly different among people with different overall weekly eating frequencies, usually an upward trend. The estimated daily intakes of antibiotics were on the levels of 0.001-1.0 µg/kg/day, mainly contributed by clarithromycin, ciprofloxacin and oxytetracycline, indicating a potential health risk based on the microbiological effect. A significantly positive correlation was found between DNA oxidative damage and exposure for four categories of antibiotics, conformed by both Spearman correlation and multiple linear regression analysis. The levels of 8-OHdG were 355 %, 239 %, 234 %, and 334 % higher with elevated levels of phenicols, macrolides, tetracyclines and sulfonamides from quartiles 2 to 4. Our results suggest that high-frequency consumption of takeaways may exacerbate oxidative stress trends through human exposure to antibiotics.

Divergence of functions and expression patterns of soybean bZIP transcription factors.

Soybean (Glycine max) is a major protein and oil crop. Soybean basic region/leucine zipper (bZIP) transcription factors are involved in many regulatory pathways, including yield, stress responses, environmental signaling, and carbon-nitrogen balance. Here, we discuss the members of the soybean bZIP family and their classification: 161 members have been identified and clustered into 13 groups. Our review of the transcriptional regulation and functions of soybean bZIP members provides important information for future study of bZIP transcription factors and genetic resources for soybean breeding.

Epigenetic regulation of photoperiodic flowering in plants.

In response to changeable season, plants precisely control the initiation of flowering in appropriate time of the year to ensure reproductive success. Day length (photoperiod) acts as the most important external cue to determine flowering time. Epigenetics regulates many major developmental stages in plant life, and emerging molecular genetics and genomics researches reveal their essential roles in floral transition. Here, we summarize the recent advances in epigenetic regulation of photoperiod-mediated flowering in Arabidopsis and rice, and discuss the potential of epigenetic regulation in crops improvement, and give the brief prospect for future study trends.

GmEID1 modulates light signaling through the Evening Complex to control flowering time and yield in soybean.

Soybean (Glycine max) morphogenesis and flowering time are accurately regulated by photoperiod, which determine the yield potential and limit soybean cultivars to a narrow latitudinal range. The E3 and E4 genes, which encode phytochrome A photoreceptors in soybean, promote the expression of the legume-specific flowering repressor E1 to delay floral transition under long-day (LD) conditions. However, the underlying molecular mechanism remains unclear. Here, we show that the diurnal expression pattern of GmEID1 is opposite to that of E1 and targeted mutations in the GmEID1 gene delay soybean flowering regardless of daylength. GmEID1 interacts with J, a key component of circadian Evening Complex (EC), to inhibit E1 transcription. Photoactivated E3/E4 interacts with GmEID1 to inhibit GmEID1-J interaction, promoting J degradation resulting in a negative correlation between daylength and the level of J protein. Notably, targeted mutations in GmEID1 improved soybean adaptability by enhancing yield per plant up to 55.3% compared to WT in field trials performed in a broad latitudinal span of more than 24°. Together, this study reveals a unique mechanism in which E3/E4-GmEID1-EC module controls flowering time and provides an effective strategy to improve soybean adaptability and production for molecular breeding.

Altered regulation of flowering expands growth ranges and maximizes yields in major crops.

Flowering time influences reproductive success in plants and has a significant impact on yield in grain crops. Flowering time is regulated by a variety of environmental factors, with daylength often playing an important role. Crops can be categorized into different types according to their photoperiod requirements for flowering. For instance, long-day crops include wheat (Triticum aestivum), barley (Hordeum vulgare), and pea (Pisum sativum), while short-day crops include rice (Oryza sativa), soybean (Glycine max), and maize (Zea mays). Understanding the molecular regulation of flowering and genotypic variation therein is important for molecular breeding and crop improvement. This paper reviews the regulation of flowering in different crop species with a particular focus on how photoperiod-related genes facilitate adaptation to local environments.

Diverse flowering responses subjecting to ambient high temperature in soybean under short-day conditions.

Flowering time is one of important agronomic traits determining the crop yield and affected by high temperature. When facing high ambient temperature, plants often initiate early flowering as an adaptive strategy to escape the stress and ensure successful reproduction. However, here we find opposing ways in the short-day crop soybean to respond to different levels of high temperatures, in which flowering accelerates when temperature changes from 25 to 30 °C, but delays when temperature reaches 35 °C under short day. phyA-E1, possibly photoperiodic pathway, is crucial for 35 °C-mediated late flowering, however, does not contribute to promoting flowering at 30 °C. 30 °C-induced up-regulation of FT2a and FT5a leads to early flowering, independent of E1. Therefore, distinct responsive mechanisms are adopted by soybean when facing different levels of high temperatures for successful flowering and reproduction.

Novel and multifaceted regulations of photoperiodic flowering by phytochrome A in soybean.

Photoperiod is an important environmental cue. Plants can distinguish the seasons and flower at the right time through sensing the photoperiod. Soybean is a sensitive short-day crop, and the timing of flowering varies greatly at different latitudes, thus affecting yields. Soybean cultivars in high latitudes adapt to the long day by the impairment of two phytochrome genes, PHYA3 and PHYA2, and the legume-specific flowering suppressor, E1. However, the regulating mechanism underlying phyA and E1 in soybean remains largely unknown. Here, we classified the regulation of the E1 family by phyA2 and phyA3 at the transcriptional and posttranscriptional levels, revealing that phyA2 and phyA3 regulate E1 by directly binding to LUX proteins, the critical component of the evening complex, to regulate the stability of LUX proteins. In addition, phyA2 and phyA3 can also directly associate with E1 and its homologs to stabilize the E1 proteins. Therefore, phyA homologs control the core flowering suppressor E1 at both the transcriptional and posttranscriptional levels, to double ensure the E1 activity. Thus, our results disclose a photoperiod flowering mechanism in plants by which the phytochrome A regulates LUX and E1 activity.

Polycyclic aromatic hydrocarbon exposure and DNA oxidative damage of workers in workshops of a petrochemical group.

The petrochemical industry has promoted the development of economy, while polycyclic aromatic hydrocarbons (PAHs) produced by the industry become the threat for environment and humans. Data on human occupational exposure in petrochemical industry are limited. In the present study, urinary hydroxylated PAH metabolites (OH-PAHs) and a biomarker of DNA oxidative damage (8-hydroxy-2'-deoxyguanosine (8-OHdG)) were measured in 546 workers of a petrochemical group in Northeast China, to investigate PAH exposure and related potential health risk. The concentrations of ∑9OH-PAH in all workers were 0.25-175 µg/g Cre with a median value of 4.41 µg/g Cre. Metabolites of naphthalene were the predominant compounds. The levels of PAH metabolites were significantly different for workers with different jobs, which were the highest for recycling workers (13.7 µg/g Cre) and the lowest for agency managers (5.12 µg/g Cre). Besides, higher levels of OH-PAHs were usually found in males and older workers. There was a dose-response relationship between levels of 8-OHdG and ∑9OH-PAHs (p < 0.01). No difference was observed in concentrations of 8-OHdG for workers of different gender or ages, work history as well as noise. Furthermore, workers simultaneously exposed to other potential pollutants and higher levels of ∑9OH-PAH had significantly higher levels of 8-OHdG compared with those in the corresponding subgroups. Our results suggested that exposure to PAHs or co-exposure to PAHs and potential toxics in the petrochemical plant may cause DNA damage. We call for more researches on the associations among noise, chemical pollution and oxidative stress to workers in the real working environment.

Parallel selection of distinct Tof5 alleles drove the adaptation of cultivated and wild soybean to high latitudes.

Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor. In particular, the genetic basis of the adaptation in wild soybean remains poorly understood. In this study, by combining whole-genome resequencing and genome-wide association studies we identified a novel locus, Time of Flowering 5 (Tof5), which promotes flowering and enhances adaptation to high latitudes in both wild and cultivated soybean. By genomic, genetic and transgenic analyses we showed that Tof5 encodes a homolog of Arabidopsis thaliana FRUITFULL (FUL). Importantly, further analyses suggested that different alleles of Tof5 have undergone parallel selection. The Tof5H1 allele was strongly selected by humans after the early domestication of cultivated soybean, while Tof5H2 allele was naturally selected in wild soybean, and in each case facilitating adaptation to high latitudes. Moreover, we found that the key flowering repressor E1 suppresses the transcription of Tof5 by binding to its promoter. In turn, Tof5 physically associates with the promoters of two important FLOWERING LOCUS T (FT), FT2a and FT5a, to upregulate their transcription and promote flowering under long photoperiods. Collectively, our findings provide insights into how wild soybean adapted to high latitudes through natural selection and indicate that cultivated soybean underwent changes in the same gene but evolved a distinct allele that was artificially selected after domestication.

Natural variation and artificial selection of photoperiodic flowering genes and their applications in crop adaptation.

Flowering links vegetative growth and reproductive growth and involves the coordination of local environmental cues and plant genetic information. Appropriate timing of floral initiation and maturation in both wild and cultivated plants is important to their fitness and productivity in a given growth environment. The domestication of plants into crops, and later crop expansion and improvement, has often involved selection for early flowering. In this review, we analyze the basic rules for photoperiodic adaptation in several economically important and/or well-researched crop species. The ancestors of rice (Oryza sativa), maize (Zea mays), soybean (Glycine max), and tomato (Solanum lycopersicum) are short-day plants whose photosensitivity was reduced or lost during domestication and expansion to high-latitude areas. Wheat (Triticum aestivum) and barley (Hordeum vulgare) are long-day crops whose photosensitivity is influenced by both latitude and vernalization type. Here, we summarize recent studies about where these crops were domesticated, how they adapted to photoperiodic conditions as their growing area expanded from domestication locations to modern cultivating regions, and how allelic variants of photoperiodic flowering genes were selected during this process. A deeper understanding of photoperiodic flowering in each crop will enable better molecular design and breeding of high-yielding cultivars suited to particular local environments. Supplementary Information: The online version contains supplementary material available at 10.1007/s42994-021-00039-0.

Molecular mechanisms for the photoperiodic regulation of flowering in soybean.

Photoperiodic flowering is one of the most important factors affecting regional adaptation and yield in soybean (Glycine max). Plant adaptation to long-day conditions at higher latitudes requires early flowering and a reduction or loss of photoperiod sensitivity; adaptation to short-day conditions at lower latitudes involves delayed flowering, which prolongs vegetative growth for maximum yield potential. Due to the influence of numerous major loci and quantitative trait loci (QTLs), soybean has broad adaptability across latitudes. Forward genetic approaches have uncovered the molecular basis for several of these major maturity genes and QTLs. Moreover, the molecular characterization of orthologs of Arabidopsis thaliana flowering genes has enriched our understanding of the photoperiodic flowering pathway in soybean. Building on early insights into the importance of the photoreceptor phytochrome A, several circadian clock components have been integrated into the genetic network controlling flowering in soybean: E1, a repressor of FLOWERING LOCUS T orthologs, plays a central role in this network. Here, we provide an overview of recent progress in elucidating photoperiodic flowering in soybean, how it contributes to our fundamental understanding of flowering time control, and how this information could be used for molecular design and breeding of high-yielding soybean cultivars.

Light-up RNA aptamer signaling-CRISPR-Cas13a-based mix-and-read assays for profiling viable pathogenic bacteria.

Viable pathogenic bacteria cause serious human diseases via systemic infections and food poisoning. Herein, we constructed a light-up RNA aptamer signaling-CRISPR-Cas13a assay enabling mix-and-read detection of viable pathogenic bacteria. Directly targeting pathogen RNAs via CRISPR-Cas13a allows precisely discriminating viable bacteria from dead bacteria. We introduced a light-up RNA aptamer, Broccoli, serving as the substate of activated CRISPR-Cas13a to monitor the presence of pathogen RNAs, eliminating the need to use chemically labeled RNA substrate. Sequentially, the assay allows a reverse transcription-free, nucleic acid amplification-free, and label-free quantification of RNA targets and viable pathogenic bacteria. It could detect as low as 10 CFU of Bacillus cereus and precisely quantify viable bacteria with a content ranging from 0% to 100% in 105 CFU total bacteria. The quantification of viable bacteria allows more accurately estimating the ability of B. cereus to spoil food. The RNA assay promises its use in point-of-use detection of viable pathogens and biosafety control.

Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication.

Adaptive changes in plant phenology are often considered to be a feature of the so-called 'domestication syndrome' that distinguishes modern crops from their wild progenitors, but little detailed evidence supports this idea. In soybean, a major legume crop, flowering time variation is well characterized within domesticated germplasm and is critical for modern production, but its importance during domestication is unclear. Here, we identify sequential contributions of two homeologous pseudo-response-regulator genes, Tof12 and Tof11, to ancient flowering time adaptation, and demonstrate that they act via LHY homologs to promote expression of the legume-specific E1 gene and delay flowering under long photoperiods. We show that Tof12-dependent acceleration of maturity accompanied a reduction in dormancy and seed dispersal during soybean domestication, possibly predisposing the incipient crop to latitudinal expansion. Better understanding of this early phase of crop evolution will help to identify functional variation lost during domestication and exploit its potential for future crop improvement.